HDF5Writer

class patato.io.hdf.hdf5_interface.HDF5Writer(file)

Bases: WriterInterface

__init__(file)

Methods

__init__(file)
add_image(image_data)
add_roi(roi_data[, generated])	Add a region of interest to the hdf5 file.
close()
delete_dso2s()	Delete the old dso2 datasets.
delete_images(image)
delete_recons([name, recon_groups])	Delete some reconstructions.
delete_rois([name_position, number])
rename_roi(old_name, new_name, new_position)	Rename a region of interest.
save_file(reader)
set_correction_factor(correction_factor)
set_impulse_response(impulse_response)
set_pa_data(raw_data)
set_repetition_numbers(repetition_numbers)
set_run_numbers(run_numbers)
set_sampling_frequency(frequency)
set_scan_comment(comment)
set_scan_datetime(datetime)
set_scan_name(scan_name)
set_scan_times(scan_times)
set_scanner_z_position(z_position)
set_segmentation(seg)
set_sensor_geometry(sensor_geometry)
set_speed_of_sound(c)
set_temperature(temperature)
set_water_absorption(water_absorption, ...)
set_wavelengths(wavelengths)

add_roi(roi_data: ROI, generated: bool = False)

Add a region of interest to the hdf5 file.

Parameters:

• roi_data (ROI)

• generated (bool, default False)

delete_dso2s()

Delete the old dso2 datasets. Might want to remove this or refactor it in some way?

delete_recons(name=None, recon_groups: Sequence[str] | None = None)

Delete some reconstructions.

Parameters:

• name (str or None)

• recon_groups ((iterable of str) or None)

rename_roi(old_name, new_name, new_position)

Rename a region of interest.

Parameters:

• old_name (str or tuple) – Old roi name e.g. “tumour_left/0” or (“tumour_left”, “0”)

• new_name (str) – New roi name e.g. “brain”

• new_position (str) – New roi position e.g. “left”